Exploration and analysis of R-loop mapping data with RLBase

Henry E. Miller, Daniel Montemayor, Janet Li, Simon A. Levy, Roshan Pawar, Stella Hartono, Kumar Sharma, Bess Frost, Frederic Chedin, Alexander J.R. Bishop

Research output: Contribution to journalArticlepeer-review


R-loops are three-stranded nucleic acid structures formed from the hybridization of RNA and DNA. In 2012, Ginno et al. introduced the first R-loop mapping method. Since that time, dozens of R-loop mapping studies have been conducted, yielding hundreds of publicly available datasets. Current R-loop databases provide only limited access to these data. Moreover, no web tools for analyzing user-supplied R-loop datasets have yet been described. In our recent work, we reprocessed 810 R-loop mapping samples, building the largest R-loop data resource to date. We also defined R-loop consensus regions and developed a framework for R-loop data analysis. Now, we introduce RLBase, a user-friendly database that provides the capability to (i) explore hundreds of public R-loop mapping datasets, (ii) explore R-loop consensus regions, (iii) analyze user-supplied data and (iv) download standardized and reprocessed datasets. RLBase is directly accessible via the following URL: https://gccri.bishop-lab.uthscsa.edu/shiny/rlbase/.

Original languageEnglish (US)
Pages (from-to)D1129-D1137
JournalNucleic acids research
Issue numberD1
StatePublished - Jan 6 2023
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


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